data integration

Identify human candidate disease genes - GenoBridge

ssuhr@ebi.ac.uk — Mon, 15 Feb 2016 13:15:30 +0000

GenoBridge

The fundamental genetic similarity between mice and humans allows researchers to infer a human gene's function based on studies with laboratory mice. Identifying essential clues on gene function provided by model organisms has proved to be a powerful approach to gain knowledge on both human disease and mammalian biology.

Data interoperability and standards

ssuhr@ebi.ac.uk — Fri, 01 May 2015 15:25:51 +0000

Standards and identifiers

Evaluating the effect of drugs by integrating clinical trials data and genomic information

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 14:01:45 +0000

The Clinical Trials Information Mediator supports researchers by providing insight into the effect of drugs on patients based on clinical trials data and genomic information.

Visualising ontologies and locating terms in a query interface

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 13:32:05 +0000

The PLATO ontology tree viewer is a plugin that supports visualization of terms in an ontology. Nodes can be expanded and collapsed as needed.

Manage cross-references between digital entities with different identifiers

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 09:37:55 +0000

myEquivalents is a system to manage cross-references between digital entities with different identifiers. It can help organisations maintaining data to manage their cross-references and aids finding multiple descriptions of the same biomedical entities.

Making sure standards are fit for purpose

ssuhr@ebi.ac.uk — Thu, 05 Feb 2015 09:33:06 +0000

The Metadata Model and Mapping Registry (MMMR) enables researchers to find a representative collection of meta-data artefacts (models, formats, minimal information guidelines, biobank data dictionaries, detailed clinical/research models) of use to the biomedical science community.

Online Dictionary of common molecular identifiers of the biomedical sciences research infrastructures

ssuhr@ebi.ac.uk — Fri, 13 Apr 2012 16:08:38 +0000

The provision and use of common and unambiguous identifiers for bio-molecules such as genes, proteins and bioactive compounds is key to supporting the information flow from basic science, model organism biology, bioinformatics and structural biology through to translational research and clinical care. The ESFRI BMS project partners have determined an interoperable ‘Dictionary’ of identifier types (Appendix 1) used in this project, and within clinical/translational research more broadly. At the request of the scientific advisory board, we have also expanded our WP3.1 activities to include the development of best practices documentation for identifiers (Appendix 2-1) which was based on our identifiers landscape analysis (Appendix 2-2). Part of the expanded work on identifiers includes a shortlist of the most relevant Identifier Resolution and Conversion Tools (Appendix 2-3); these have also been registered with the BioMedBridges Tools and Data Services Registry. Further documentation was developed to guide the selection of ontologies (Appendix 2-4) to support cross-domain data integration. Where no authoritative identifier standard exists, we have worked with the respective community to determine one that would support the activities of WP4 and BioMedBridges use cases. Relevant identifiers include those for samples (Task 2), small molecules, macromolecular assemblies, genes, proteins, drugs, diseases and phenotypes.